Variant report

Variant	rs17035504
Chromosome Location	chr12:104781613-104781614
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:104680831..104683317-chr12:104781247..104783263,2	K562	blood:

Variant related genes	Relation type
ENSG00000198431	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10735392	0.86[CEU][hapmap];0.87[MEX][hapmap]
rs10735393	0.86[CEU][hapmap]
rs10745995	0.86[CEU][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap]
rs10745996	0.86[CEU][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap]
rs10861204	0.86[CEU][hapmap]
rs10861216	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12425334	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12425523	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13377715	0.87[ASN][1000 genomes]
rs17035521	0.83[EUR][1000 genomes]
rs17202862	0.93[CEU][hapmap]
rs1922264	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3935021	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4129598	1.00[MKK][hapmap]
rs4246269	0.86[CEU][hapmap]
rs4246271	0.86[CEU][hapmap]
rs4403872	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4545635	1.00[MKK][hapmap]
rs4614534	1.00[MKK][hapmap]
rs4630362	0.92[CEU][hapmap]
rs4964288	0.86[CEU][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap]
rs4964752	0.86[CEU][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap]
rs4964761	0.86[CEU][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap]
rs4964779	0.86[CEU][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap]
rs4964789	0.83[ASN][1000 genomes]
rs56831540	0.95[ASN][1000 genomes]
rs57710522	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57954752	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59348790	0.85[ASN][1000 genomes]
rs60394569	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6539137	0.83[CEU][hapmap]
rs7138035	0.82[CEU][hapmap]
rs7294997	0.83[CEU][hapmap]
rs73183716	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73183722	0.81[EUR][1000 genomes]
rs73183723	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7486552	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7962423	0.86[CEU][hapmap]
rs9739833	0.86[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899494	chr12:104561521-104806232	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17035504	HCFC2	cis	cerebellum	SCAN
rs17035504	NFYB	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104776400-104782400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr12:104778200-104801400	Weak transcription	A549	lung
3	chr12:104779600-104787600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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